Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor

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Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor through the Molecular Combination of Chemotype Distinct Screening Hits Mark E. Schnute, Matthew D. McReynolds, Jeffrey Carroll, Jill E Chrencik, Maureen K. Highkin, Kaliapan Iyanar, Gina Jerome, John W. Rains, Matthew Saabye, Jeffrey A. Scholten, Matthew Yates, and Marek M. Nagiec J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.7b00070 • Publication Date (Web): 23 Feb 2017 Downloaded from http://pubs.acs.org on February 24, 2017

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Journal of Medicinal Chemistry

Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor through the Molecular Combination of Chemotype Distinct Screening Hits Mark E. Schnute*,† Matthew D. McReynolds,† Jeffrey Carroll,† Jill Chrencik,§ Maureen K. Highkin,‡ Kaliapan Iyanar,† Gina Jerome,‡ John W. Rains,‡ Matthew Saabye,‡ Jeffrey A. Scholten,† Matthew Yates,‡ and Marek M. Nagiec‡ †Medicine Design and ‡Inflammation and Immunology Research, Pfizer, Cambridge, Massachusetts 02139, United States §Medicine Design, Pfizer, Groton, Connecticut 06340, United States

KEYWORDS: Sphingosine kinase, SphK1, SphK2, sphingosine-1-phosphate, S1P, high throughput screening

ABSTRACT: Sphingosine kinase (SphK) is the major source of the lipid mediator and GPCR agonist sphingosine-1-phosphate (S1P). S1P promotes cell growth, survival and migration and is a key regulator of lymphocyte trafficking. Inhibition of S1P signaling has been proposed as a strategy for treatment of inflammatory diseases and cancer. Two different formats of an enzyme

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based high-throughput screen yielded two attractive chemotypes capable of inhibiting S1P formation in cells. The molecular combination of these screening hits led to compound 22a (PF543) with two orders of magnitude improved potency. Compound 22a inhibited SphK1 with an IC50 of 2 nM and was more than 100-fold selective for SphK1 over the SphK2 isoform. Through the modification of tail region substituents, the specificity of inhibition for SphK1 and SphK2 could be modulated yielding SphK1 selective, potent SphK1/2 dual, or SphK2 preferential inhibitors.

INTRODUCTION The sphingosine kinases (SphK) are a family of lipid kinases that are responsible for the phosphorylation of sphingosine (1a) to afford sphingosine-1-phosphaste (S1P, 1b), Figure 1.1 S1P is an important bioactive lipid signaling molecule that acts as an agonist to five specific G protein-coupled receptors (S1PR1‒5) as well as displaying intracellular secondary messenger actions.2

S1P has a wide range of biological functions including promotion of cellular

proliferation and survival, immune cell trafficking, stimulation of angiogenesis, and regulation of vascular integrity.3-5 As a consequence, its production and function as part of the SphK‒S1P‒ S1PR axis has profound implications towards human disease in the fields of inflammatory disorders, cardiovascular disease, and oncology. Two isoforms of SphK are found in mammalian organisms, SphK1 and SphK2.6,7 SphK1 (42 kDa) is found primarily in the cytoplasm and the plasma membrane of erythrocyte, endothelial and mast cells. On the other hand, SphK2 is larger (63 kDa) and localized to the endoplasmic reticulum, nucleus, and mitochondria. SphK1 and SphK2 demonstrate redundancy in function


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since Sphk1–/‒ and Sphk2–/‒ mice independently are healthy and fertile while elimination of both genes is embryonically lethal.8,9 Marked differences however have been observed between the two transgenic strains towards plasma S1P levels. Sphk1–/‒ mice display significantly reduced S1P levels (50%) in the plasma while Sphk2–/‒ mice actually show S1P levels 3-4 fold higher than wild type animals.8,10-12 The latter suggests a much more complex pharmacological role for SphK2 than simply producing S1P, which has yet to be fully elucidated. The therapeutic potential of targeting the S1P regulatory pathway has been best demonstrated by the S1P1 receptor agonist fingolimod (FTY-720, 2-amino-2-(2-(4-octylphenyl)ethyl)-1,3propanediol).13 Fingolimod is a “functional antagonist” of the receptor since its binding leads to receptor internalization and degradation, and agonist signaling through the S1P1 receptor by S1P is required for lymphocyte egress in inflammatory disease. Efficacy in a variety of preclinical autoimmune models has been reported for fingolimod through its ability to block this signalling.13 In humans, fingolimod has been shown to induce lymphopenia and is approved for the treatment of relapsing remitting multiple sclerosis.14,15 Consequently, the reduction of circulating or tissue specific S1P levels through the inhibition of SphK has also been envisioned to have the potential to impact disease. Sphk1–/‒ mice were reported to show decreased synovial inflammation in a TNF-α–induced arthritis model; however, Sphk2–/‒ mice displayed more severe disease in the same model suggesting a SphK1 inhibitor may be preferred for the potential treatment of rheumatoid arthritis.16,17 Sphk1–/‒ mice were also reported to be less susceptible to colitis induced by dextran sodium sulfate (DSS), a preclinical model of irritable bowel disease (IBD).18

S1P and SphK1 may also play a role in the

development of fibrosis.19 Expression of SphK1 negatively correlates with lung function and survival for patients with idiopathic pulmonary fibrosis (IPF), and Sphk1–/‒ mice were reported to


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be protected from disease symptoms in the bleomycin model of fibrosis.20 A two-fold elevation of SphK1 has been reported in the livers of patients with non-alcoholic fatty liver disease suggesting S1P may promote hepatic inflammation.21 In a preclinical model of non-alcoholic steatohepatitis (NASH), Sphk1–/‒ mice were protected from disease. Also, wild type diabetic mice were reported to exhibit increased renal cortical S1P and renal fibrosis markers compared to SphK1 deficient diabetic mice.22 In recent studies, inhibition of SphK1 ameliorated cardiac hypertrophy and dysfunction in hypoxic models of myocardial infarction and pulmonary arterial hypertension.23,24 SphK1 has been found to be overexpressed in many types of cancerous tumors.25-27 S1P produced by SphK1 is believed to contribute to prosurvival and antiapoptotic mechanisms as well as chemotherapy resistance. However, the translation of SphK inhibitors to reduced cancer cell survival has not been straightforward.28 Recently, S1P levels have been reported to be elevated in the blood of mice and humans with sickle cell disease (SCD), and SphK1 inhibition by an inhibitor or siRNA resulted in reduced cell sickling.29 The evolution of SphK1 and SphK2 inhibitors has been recently reviewed.30-32 Many SphK inhibitors mimic the substrate (sphingosine, 1a) in that they have a polar head group and a lipophilic tail region. One such example is compound 2 reported by Genzyme to be a potent SphK1 inhibitor (IC50 = 58 nM), Figure 2.33 The first co-crystal structure of SphK1 with an inhibitor was reported by Amgen utilizing compound 3a (SphK1 IC50 = 20 nM, SphK2 IC50 = 1.6 µM).34 They also found that a related analog 3b reduced plasma S1P levels when dosed orally in mice. Researchers at the University of Virginia and Virginia Tech have reported a series of amidine and guanidine-based SphK inhibitors represented by 4a and 4b.35-37 Compound 4b was a potent inhibitor of SphK1 (IC50 = 48 nM) while being highly selective for SphK2 (IC50 > 10 µM). On the other hand, removal of the methylene linker as in compound 4a


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afforded one of the most potent SphK2 selective compounds reported (SphK1 IC50 = 13 µM, SphK2 IC50 = 1.3 µM). Efforts to decipher the complex pharmacology between SphK1 and SphK2 will require a range of potent inhibitor tool compounds consisting of SphK1 selective, SphK2 selective and SphK1/2 dual inhibitors.

By employing high throughput screening

methodology, we have identified two SphK inhibitor chemotypes. Subsequent optimization strategies including molecular combination of these two series was successful in identifying highly potent SphK1 selective and SphK1/2 dual inhibitors as well as compounds favoring SphK2 inhibition.

RESULTS AND DISCUSSION Screening Strategy In order to provide the broadest opportunity to identify SphK inhibitors, we screened the Pfizer compound collection using two different formats of a recombinant enzyme assay. In one approach, a screening subset (ca. 150 000 compounds) was screened for a compound′s ability to inhibit the production of FITC-S1P by purified human SphK1 using a microfluidic mobility-shift separation system (Caliper Life Sciences).38 In parallel, a Transcreener® ADP detection assay based on fluorescent polarization derived from binding of a fluorescent ADP derivative to an anti-ADP antibody was used to screen a second unique compound subset (ca. 400 000 compounds) for the inhibition of ADP formation resulting from the enzyme reaction.38 Both compound collections were a diverse subset of the larger Pfizer compound file. The selection of the compound collection with respect to assay was based on the screening capacity of the individual assay. Subsequent confirmation using a dose response in the corresponding assay


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yielded approximately 800 compounds (0.5% hit rate) from the Caliper® assay screen and approximately 350 compounds (0.09% hit rate) from the Transcreener® assay screen with an IC50 < 10 µM. Representative compounds from each distinct hit set were then assayed in the respective orthogonal assay revealing a poor translation between the two recombinant enzyme assays. In addition, a diverse set of compounds identified through the Caliper® assay screen all showed a similar potency shift with respect to increased enzyme concentration. Both of these observations suggested a potentially high artifact rate from one or more of the screening approaches. The necessity to replicate the lipid associated environment native to SphK1 function in a recombinant enzyme system (e.g. high detergent concentrations) may have contributed to these findings. Therefore, a more physiologically relevant cell based assay was considered to further hit validation. Head and neck carcinoma 1483 cells were found to demonstrate a high conversion rate of C17sphingosine to C17-S1P. Also, a high ratio of SphK1 to SphK2 mRNA (700x) in these cells suggested that SphK1 was the dominant isoform of S1P production. Subsequent triage efforts focused on hit series which demonstrated potency in both recombinant enzyme assay formats as well as displaying the ability to inhibit C17-S1P production in 1483 cells. Gratifyingly, this effort identified two attractive hit chemotypes, one from each enzyme screening assay format, Figure 3. The first chemotype, the “aminobenzimidazole” series represented by compound 12, was identified from the Caliper® assay format. The second chemotype, the “benzylpyrrolidine” series represented by 20a, was identified from the Transcreener® assay.


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Aminobenzimidazole Series The screening hit 12 was synthesized as described in Scheme 1 through a convergent route forming the ether bond as the pivotal step. The required phenol was prepared from 3(bromomethyl)-5-methylphenylacetate (5) by nucleophilic displacement of the bromide by the sodium salt of phenylsulfinic acid to provide sulfone 6. Phenol 7 was then obtained by basic hydrolysis of the acetate protecting group. Diamine 8 was condensed with 1,3-bis(tertbutoxycarbonyl)-2-methyl-2-thiopseudourea to provide the nitrogen-protected aminobenzimidazole 9. The ester was then reduced to afford alcohol 10 which facilitated Mitsunobu coupling with phenol 7. Compound 12 was then obtained after deprotection. Similarly, the corresponding benzimidazole 15 was prepared by alkylation of phenol 6 with alkylchloride 14 which was prepared from alcohol 13, Scheme 2. Compound 12 demonstrated similar potencies in both the Caliper® and Transcreener® recombinant enzyme assays (IC50 = 1.4 µM and 1.7 µM, respectively). Only modest potency was observed against SphK2 (IC50 = 39.6 µM). Compound 12 inhibited the production of C17S1P in 1483 cells (IC50 = 180 nM) with no indication of cellular toxicity (MTT, 50 µM). Excellent kinome selectivity was observed (90 kinases, < 50% inhibition, 10 µM dose), and the compound did not bind to representative S1P receptors (S1P1-3,5; IC50 > 10 µM). Unfortunately due to low solubility, attempts to provide evidence of direct binding of compound 12 to SphK1 through ITC measurements were unsuccessful. The amino-substituent on the benzimidazole was found to be essential for SphK inhibition since compound 15 demonstrated significantly reduced potency in both the recombinant enzyme and cellular assays (IC50 = 48 µM and 27 µM, respectively).


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Benzylpyrrolidine Series The screening hit 20a and subsequent analogs were prepared as described in Scheme 3. The coupling of 4-bromo-2-fluoro-1-nitrobenzene with (4-formylphenyl)boronic acid afforded biaryl 17. The amine functionality was next installed through reductive amination of the aldehyde with pyrrolidine or 2-(hydroxymethyl)pyrrolidine to provide intermediates represented by compound 18. Benzimidazoles 20a-j were then prepared by displacement of the fluorine with a corresponding primary alkylamine (H2NRʹ), condensation with acetaldehyde and reductive ring closure. We prepared all four diastereomers of the screening hit in stereodefined configurations and assessed their ability to inhibit SphK1 and SphK2, Table 1. Diastereomer 20a was found to be the most potent isomer with similar inhibitory potency in both the SphK1 Caliper® and Transcreener® recombinant enzyme assays (IC50 = 0.87 µM and 0.19 µM, respectively). It was also a potent inhibitor of C17-S1P production in 1483 cells (IC50 = 0.081 µM) and demonstrated excellent kinome selectivity (89 kinases, < 50% inhibition, 10 µM dose). The other three diastereomers (20b-d) all showed weaker potency in all three assays with similar rank ordering. The stereospecificity of kinase inhibition demonstrated between 20a and 20d provided strong support for validation of the hit as directly interacting with SphK1. This was further supported by evidence of direct binding of 20a to SphK1 as measured through ITC (Kd = 2.9 µM) and a corresponding weaker affinity for 20b consistent with the functional assays. The influence of the benzimidazole nitrogen substituent on SphK1 potency was explored in analogs 20e-i, Table 2. More hydrophobic substituents that were either isosteric (20g) or larger (20e,f) than the tetrahydrofuranylmethyl of 20a showed a profound improvement in potency. The increased potency of 20e-g, however, was offset by the increased lipophilicity of the


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molecules as demonstrated by a reduction in the LIPE compared to compound 20a, Table 2. On the other hand, replacing the saturated ring by phenyl (20h) or reducing the size of the substituent (20i) was detrimental to potency. As demonstrated by compound 20j, the hydroxymethyl substituent of the pyrrolidine ring was critical for SphK1 inhibition. Based on the structure-activity relationship for these and other analogs in the series, a strong correlation between inhibition of the recombinant enzyme and inhibition of C17-S1P production in 1483 cells was observed (R2 = 0.924, n = 60), Figure 4. This correlation provided further support that compound 20a and related analogs are acting through inhibition of SphK1 to result in cellular suppression of S1P production.

Lead-hopping through molecular combination It is tempting to consider the benzimidazole present in both 12 and 20a as a common substructure when aligning the two chemotypes. However, it is important to consider the structure-activity learnings for each series along with the nature of the endogenous ligand, sphingosine – a molecule with a polar amine head and lipophilic tail. For compound 20a, the 2(hydroxymethyl)pyrrolidine group is assumed to mimic the aminoalcohol head of sphingosine and the substituted benzimidazole represents the lipophilic tail consistent with the critical contribution of both regions to potency of the molecule. ROCS alignment39 of compounds 12 and 20a based on both shape and functional group chemistry suggested the aminoimidazole fragment of 12 indeed represented the polar terminus, Figure 5. This proposal would be consistent with the loss of potency observed in replacing the amino group by hydrogen (15). The alignment suggested the possibility of combining the hydrophobic tail of 12, i.e.


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((phenylsulfonyl)methyl)phenoxy, with the polar head group of 20a, i.e. (1-benzylpyrrolidin-2yl)methanol, Figure 3. The resulting combination was compound 22a (PF-543),38,40 Table 3. Compound 22a and related analogs based on this hypothetical combination were prepared as shown in Scheme 4. A substituted phenol such as 7 was alkylated by 4-bromomethylbenzaldehyde, and the resulting aldehyde was then reacted with a corresponding amine under reductive alkylation conditions. Indeed compound 22a, the product of direct combination of 12 and 20a, was found to be a potent inhibitor of SphK1 in recombinant enzyme assays, Table 3. Compared to compound 20a, a 100-fold improvement in cellular potency for inhibition of C17S1P production was obtained (IC50 = 0.8 nM). Similarly, LIPE improved to 6.8 (∆LIPE = 2.0) since the partition coefficient remained comparable to 20a (22a, measured LogD = 2.3). Compound 22a also inhibited the production of C17-S1P in a human whole blood ex-vivo assay (IC50 = 20 nM).41 Excellent kinome selectivity was observed (90 kinases,

Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor

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